Effect of nitrate uptake rate on growth and glycogen production.

<p>The specific growth rate (solid line) and glycogen production rate (dashed line) at each nitrate uptake rate are shown. The dotted line indicates the optimal uptake rate for biomass production. The grey area represents the solution space of the glycogen production rate calculated by flux variability analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144430#pone.0144430.ref038" target="_blank">38</a>], as the glycogen production rate was undetermined.</p

Comparison of the growth capabilities on the various organic substrates.

<p>Comparison of the growth capabilities on the various organic substrates.</p

Flux response analysis for glycogen production.

<p>The simulated metabolic flux distribution under autotrophic conditions is shown (A). The values indicate the metabolic flux of each reaction. The flux was normalized to that of the reaction catalyzed by ribulose 1,5-bisphosphate carboxylase/oxygenase. Bold and dashed-bold arrows indicate the reactions whose activation or repression increased glycogen production, respectively, identified by flux response analysis. The reactions “DHAP + E4P ↔ S7P”, “DHAP + G3P ↔ F6P” and “G3P + S7P ↔ E4P + F6P” were undetermined, and the flux range of these reactions was calculated by flux variability analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144430#pone.0144430.ref038" target="_blank">38</a>]. FRA results of the phosphoglucomutase reaction (G6P → G1P) (B) and phosphoenolpyruvate carboxylase reaction (PEP → Oxa) (C) are shown. The X-axis indicates the flux of the corresponding reaction and the Y-axis indicates the glycogen production rate excluding the flux for biomass production, as glycogen is a component of the biomass. The dotted line indicates the optimal flux of the corresponding reaction. The grey area in Fig 3(C) represents the solution space calculated by flux variability analysis. 2PG, glycerate-2-phosphate; 3PG, 3-phosphoglycerate; 6PGC, 6-phospho-gluconate; 6PGL, 6-phospho-glucono-1,5-lactone; AcCoA, acetyl-CoA; αKG, α-ketoglutarate; Cit, citrate; DHAP, dihydroxyacetone phosphate; E4P, erythrose-4-phosphate; F6P, fructose-6-phosphate; Fum, fumarate; G1P, glucose-1-phosphate; G3P, glyceraldehyde-3-phosphate; G6P, glucose-6-phosphate; Icit, isocitrate; Mal, malate; Oxa, oxalate; PEP, phosphoenolpyruvate; Pyr, pyruvate; R5P, ribose-5-phosphate; Ru5P, ribulose-5-phosphate; RuBP, ribulose-1,5-bisphosphate; S7P, sedoheptulose-7-phosphate; Suc, succinate; Sucsal, succinyl semialdehyde; Xu5P, xylulose-5-phosphate.</p

Culture profile under nitrogen depletion conditions.

<p>Growth and intracellular glycogen (A) together with the concentrations of organic acids in the culture medium (B) were summarized. Closed circle, OD₇₅₀; open circle, glycogen content; square, acetate; diamond, lactate; triangle, pyruvate. Error bars represent the standard deviation of triplicate experiments.</p

Characteristics of the reconstructed metabolic model of <i>A</i>. <i>platensis</i> NIES-39.

<p>The number of unique metabolites was calculated by considering the metabolites present in more than one compartment as a single metabolite.</p

<i>In silico</i> knockout simulation for ethanol production with nitrate as nitrogen source.

<p>Detailed information is summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144430#pone.0144430.s004" target="_blank">S4 Table</a>.</p

<i>In silico</i> knockout simulation for ethanol production with ammonium as nitrogen source.

<p>Detailed information is summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144430#pone.0144430.s004" target="_blank">S4 Table</a>.</p

Core2 β-1,6-<i>N</i>-acetylglucosaminyltransferase-1 expression correlates with prostate cancer progression.

<p>(<b>A</b>) Biosynthetic pathways for <i>O</i>-glycans. (<b>B</b>) PCa specimens were incubated with an anti-core2 β-1,6-<i>N</i>-acetylglucosaminyltransferase-1 (GCNT1) monoclonal antibody (mAb), followed by a horseradish peroxidase (HRP)-conjugated secondary antibody. Counterstaining was performed using hematoxylin. GCNT1-positive cancer cells are brown. (<b>C</b>) Prostate-specific antigen-free survival periods were compared between GCNT1-positive and GCNT1-negative specimens. Survival was analyzed using Kaplan-Meier curves.</p

Prostate-specific antigen concentration and core2 β-1,6-<i>N</i>-acetylglucosaminyltransferase-1 expression predict extracapsular extension of prostate cancer.

<p>(<b>A</b>) Prostate-specific antigen (PSA) concentration and (<b>B</b>) Core2 β-1,6-<i>N</i>-acetylglucosaminyltransferase-1 (GCNT1) expression levels were significantly higher in prostate cancer (PCa) patients with extracapsular extension than in patients with organ-confined disease. (<b>C</b>) Receiver-operator characteristic curve analysis of PSA and GCNT1 revealed that the area under the curve of PSA was 0.7455 and GCNT1 was 0.7614. (<b>D</b>) Risk stratification was established using PSA and GCNT1 to predict the outcome of local PCa. Double negative (DN)-risk (PSA < 7.52 ng/mL, GCNT1< 79.36 pg/mg), single positive (SP)-risk (PSA > 7.52 ng/mL or GCNT1 > 79.36 pg/mg) and double positive (DP)-risk (PSA > 7.52 ng/mL and GCNT1 > 79.36 pg/mg) patients are compared.</p

Logistic regression analyses of risk factors for extracapsular extension of prostate cancer.

<p>^a; pre-treatment prostate-specific antigen</p><p>^b; Gleason score</p><p>CI, confidence interval; GCNT1, core2 β-1,6-<i>N</i>-acetylglucosaminyltransferase-1; HR, hazard ratio; PSA, prostate-specific antigen</p><p>Logistic regression analyses of risk factors for extracapsular extension of prostate cancer.</p